Here's one way:

#!/usr/bin/env perl

use warnings;
use strict;
use Data::Dumper;
my $string = '1,3,5,7,9,1,3,4,5,6,2,1,5,6,7,9';
my @numbers = sort split /,/, $string;
my %seen;
for (@numbers) {
    if ($seen{$_}) {
        $seen{$_} += 1;
    }
    else {
        $seen{$_} = 1;
    }
}
print "@numbers\n";
print Dumper(\%seen);
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